sand_filter_kernel - filter read sequences sequentially

       The  Cooperative  Computing  Tools are Copyright (C) 2022 The University of Notre Dame.  This software is
       distributed under the GNU General Public License.  See the file COPYING for details.

sand_filter_kernel  filters  a list of genomic sequences, and produces a list of candidate pairs for more
       detailed alignment.  It is not normally called by the user, but is invoked by  sand_filter_master(1)  for
       each sequential step of a distributed alignment workload.

       If  one  sequence  file  is given, sand_filter_kernel will look for similarities between all sequences in
       that file.  If given two files, it will look for similarities between sequences in the first file and the
       second file.  The output is a list of candidate pairs, listing the name of the candidate sequences and  a
       starting position for alignment.

       Users do not normally invoke sand_filter_kernel directly.  Instead,  options  such  as  the  k-mer  size,
       minimizer  window,  and  repeat  file  may  be  specified  by the same arguments to sand_filter_master(1)
       instead.  For example, to run a filter with a k-mer size of 20, window size of 24,  and  repeat  file  of
       mydata.repeats:

               % sand_filter_master -k 20 -w 24 -r mydata.repeats mydata.cfa mydata.cand

       On success, returns zero.  On failure, returns non-zero.

sand_filter_kernel - filter read sequences sequentially

-s<size>
              Size  of  "rectangle" for filtering. You can determine the size dynamically by passing in d rather
              than a number.

        -r<file>
              A meryl file of repeat mers to be ignored.

        -k<size>
              The k-mer size to use in candidate selection (default is 22).

        -w<number>
              The minimizer window size to use in candidate selection (default is 22).

        -o<filename>
              The output file. Default is stdout.

        -d<subsystem>
              Enable debug messages for this subsystem.  Try -dall to start.

        -v    Show version string.

        -h    Show help screen.

       •   CooperativeComputingToolsDocumentation

       •   SANDUserManual

       •   sand_filter_master(1)sand_filter_kernel(1)sand_align_master(1)sand_align_kernel(1)sand_com‐press_reads(1)sand_uncompress_reads(1)work_queue_worker(1)

CCTools 7.14.5 FINAL                                                                       sand_filter_kernel(1)

       sand_filter_kernel [options] <sequencefile> [second sequence file]